benchmark · task

Protein–ligand pose prediction

This paper-specific evaluation tests Protein–ligand pose prediction using PLINDER-L95.

At a glance

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. This does not change the review status of its results.

Data, procedure and scoring
Property	Description and evidence
Record type	Paper-specific task; protocol incompletely extractedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column; Table 1, DiffDock row, Ligand RMSD (Å) column
Inputs	PLINDER-L95Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column; Table 1, DiffDock row, Ligand RMSD (Å) column
Assessment	Median ligand RMSDImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column; Table 1, DiffDock row, Ligand RMSD (Å) column
Recorded split or evaluation setting	UnextractedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column; Table 1, DiffDock row, Ligand RMSD (Å) column
Datasets	Not extracted or verified for this record.
Organisms	Not extracted or verified for this record.
Assays	Not extracted or verified for this record.
Adaptation	Not extracted or verified for this record.
Baselines	Not extracted or verified for this record.

How it works

Reported evaluation outline

Outline of the existing paper extraction. Split membership, fitting details and scorer implementation remain incompletely reviewed.

Read the diagram as text

PLINDER-L95
Recorded fitting or scoring procedure
Assess Median ligand RMSD

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column; Table 1, DiffDock row, Ligand RMSD (Å) column

Evaluation context

The existing paper extraction describes: All entries; authors note this dataset contains structures seen during model training.; All entries; rigid-protein docking comparator; authors note this dataset contains structures seen during model training. This description is retained with the exact evaluation records; it is not a new protocol reconstruction.

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column; Table 1, DiffDock row, Ligand RMSD (Å) column

Tested models and results

Release 2026-09-16-d74d282221a9 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.

Evaluated configurationMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
Boltz-1: Protein–ligand pose prediction Model: Boltz-1 · Benchmark: Protein–ligand pose prediction · Dataset: PLINDER-L95 All entries; authors note this dataset contains structures seen during model training. Independent external evaluation · Evaluation metadata: needs review
1.393 Median ligand RMSD Unit: Å · Direction: unknown	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column Source checking is not independent reproduction.
DiffDock: Protein–ligand pose prediction Model: DiffDock · Benchmark: Protein–ligand pose prediction · Dataset: PLINDER-L95 All entries; rigid-protein docking comparator; authors note this dataset contains structures seen during model training. Independent external evaluation · Evaluation metadata: needs review
1.342 Median ligand RMSD Unit: Å · Direction: unknown	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, DiffDock row, Ligand RMSD (Å) column Source checking is not independent reproduction.

Strengths and limitations

Strengths and considerations

The linked evaluation identifies the paper-specific dataset and assessment rather than treating the task name as a universal benchmark.Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column; Table 1, DiffDock row, Ligand RMSD (Å) column

Limitations and conditions

The numerical table check does not establish the full data-processing, fitting or leakage-control protocol.Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column; Table 1, DiffDock row, Ligand RMSD (Å) column

Profile review details

Catalogue extraction inspected; protocol claims remain limited to the cited evidence. Missing details are not presumed absent from the original paper.

Stable record: reported-task-bf513ed6db92c5

Sources and history

Release 2026-09-16-d74d282221a9 · Record review: needs review

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Original source · version of record

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Technical metadata and extraction receipts

Stable ID: reported-task-bf513ed6db92c5

areas: molecular-interactions
tasks: Protein–ligand pose prediction
entity level: task
version: Not reported
task: Protein–ligand pose prediction
scope note: Paper-specific evaluation task; protocol completeness requires further extraction.
missing metadata: protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract

Related records

dataset: PLINDER-L95
benchmark: Boltz-1: Protein–ligand pose prediction
benchmark: DiffDock: Protein–ligand pose prediction

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